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Conserved domains on  [gi|16131259|ref|NP_417840|]
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putative PLP-binding protein YhfX [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

YhfX family PLP-dependent enzyme( domain architecture ID 10160083)

YhfX family PLP-dependent enzyme similar to Escherichia coli pyridoxal 5'-phosphate (PLP)-dependent protein YhfX, which is a predicted amino acid racemase involved in amino acid transport and metabolism

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PLPDE_III_yhfX_like cd06811
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX; This subfamily is composed of the ...
1-382 0e+00

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX; This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.


:

Pssm-ID: 143486  Cd Length: 382  Bit Score: 655.88  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259   1 MFVEALKRQNPALISAALSLWQQGKIAPDSWVIDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYSG 80
Cdd:cd06811   1 MFLEALLKRNPALIEAALTLHQSGAIPPDTYVIDLDQIEENARLLAETAEKYGIELYFMTKQFGRNPFLARALLEAGIPG 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  81 IVAVDYKEARVMRRAGLPVAHQGHLVQIPCHQVADAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDDFLY 160
Cdd:cd06811  81 AVAVDFKEARALHEAGLPLGHVGHLVQIPRHQVPAVLAMRPEVITVYSLEKAREISDAAVELGRVQDVLLRVYGDEDTLY 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 161 PGQESGFALKVLPEIVAEIQNLPGLHLAGLTHFPCLLWDEAVGKVLPTPNLHTLIQARDQLAKSGIALEQLNAPSATSCT 240
Cdd:cd06811 161 PGQEGGFPLEELPAVLAAIKALPGIRIAGLTSFPCFLYDEEQGDIAPTPNLFTLLKAKELLEKRGIEILQLNAPSATSCA 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 241 SLPLLAQYGVTHAEPGHALTGTIPANQQGDQPERIAMLWLSEISHHFRGDSYCYGGGYYRRGHAQHALVFTPENQKITET 320
Cdd:cd06811 241 TLPLLAEYGVTHGEPGHALTGTTPLHAVGDQPEKPAMVYVSEVSHTFGGHSYCYGGGFYRRSHLKNALVGTDPDDASAHR 320
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16131259 321 NLkTVDDSSIDYTLPLAGE-FPVSSAVVLCFRTQIFVTRSDVVLVSGIHRGEPEIVGRYDSLG 382
Cdd:cd06811 321 AE-LLDPENIDYYGTLDGPeFAVGDTVIMAFRTQIFVTRSDVALVSGIASGKPRLVGIYDSQG 382
 
Name Accession Description Interval E-value
PLPDE_III_yhfX_like cd06811
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX; This subfamily is composed of the ...
1-382 0e+00

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX; This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.


Pssm-ID: 143486  Cd Length: 382  Bit Score: 655.88  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259   1 MFVEALKRQNPALISAALSLWQQGKIAPDSWVIDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYSG 80
Cdd:cd06811   1 MFLEALLKRNPALIEAALTLHQSGAIPPDTYVIDLDQIEENARLLAETAEKYGIELYFMTKQFGRNPFLARALLEAGIPG 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  81 IVAVDYKEARVMRRAGLPVAHQGHLVQIPCHQVADAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDDFLY 160
Cdd:cd06811  81 AVAVDFKEARALHEAGLPLGHVGHLVQIPRHQVPAVLAMRPEVITVYSLEKAREISDAAVELGRVQDVLLRVYGDEDTLY 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 161 PGQESGFALKVLPEIVAEIQNLPGLHLAGLTHFPCLLWDEAVGKVLPTPNLHTLIQARDQLAKSGIALEQLNAPSATSCT 240
Cdd:cd06811 161 PGQEGGFPLEELPAVLAAIKALPGIRIAGLTSFPCFLYDEEQGDIAPTPNLFTLLKAKELLEKRGIEILQLNAPSATSCA 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 241 SLPLLAQYGVTHAEPGHALTGTIPANQQGDQPERIAMLWLSEISHHFRGDSYCYGGGYYRRGHAQHALVFTPENQKITET 320
Cdd:cd06811 241 TLPLLAEYGVTHGEPGHALTGTTPLHAVGDQPEKPAMVYVSEVSHTFGGHSYCYGGGFYRRSHLKNALVGTDPDDASAHR 320
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16131259 321 NLkTVDDSSIDYTLPLAGE-FPVSSAVVLCFRTQIFVTRSDVVLVSGIHRGEPEIVGRYDSLG 382
Cdd:cd06811 321 AE-LLDPENIDYYGTLDGPeFAVGDTVIMAFRTQIFVTRSDVALVSGIASGKPRLVGIYDSQG 382
YhfX COG3457
Predicted amino acid racemase [Amino acid transport and metabolism];
26-370 2.94e-125

Predicted amino acid racemase [Amino acid transport and metabolism];


Pssm-ID: 442680 [Multi-domain]  Cd Length: 356  Bit Score: 365.28  E-value: 2.94e-125
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  26 IAPDSWVIDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYSGIVAVDYKEARVMRRAGLPvaHQGHL 105
Cdd:COG3457   1 IPPPTLVIDLDKIRENARRLVELAAKHGIELYGVTKQFGGNPEIAKALLDGGIKGIVDSRIKNLKKLKRAGIP--HPGHL 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 106 VQIPCHQVADAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDDflypgQESGFAlKVLPEIVAEIQNLPGL 185
Cdd:COG3457  79 LRIPMLSEVEEVVRYADISLNSELETARALSEAAKKQGKVHKVILMVDLGDL-----REGGFP-EELVDTVEEILKLPGI 152
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 186 HLAGL-THFPCLlwdeavGKVLPT-PNLHTLIQARDQL-AKSGIALEQLNAPSAtscTSLPLLAQ----YGVTHAEPGHA 258
Cdd:COG3457 153 ELAGLgTNLPCF------GGVLPTeENLGTLLELAELLeAKFGIKLPIVSGGNS---TSLPLLAEgtlpKGINHLRPGEA 223
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 259 LT-GTIPANQ-QGDQPERIAMLWLSEISHHFR--------------GDSYCYGggyyRRGHAQHALVFTPEnQKITETNL 322
Cdd:COG3457 224 LLlGTDPLNArPIPGLEQDAFVLVAEIIELKEkpsvpigeigrdafGNAPEFG----DRGIRKRAILAIGR-QDVDPEGL 298
                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 16131259 323 KTVDD------SSIDYtLPLAGEF-----PVSSAVVLCFRTQIFVTRSDVVLVSGIHRG 370
Cdd:COG3457 299 TPIDYgieilgASSDH-LILDVTDskedyKVGDTVVFCLRYQAFLTRSTSAYVEKIYSG 356
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
33-264 3.71e-27

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 107.31  E-value: 3.71e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259    33 IDVDQILENGKRLIETARlYGIELYLMTKQFGRNPWL---AEKLLALGYSGIVAVDYKEARVMRRAGL--PVAHQGHlvq 107
Cdd:pfam01168   1 IDLDALRHNLRRLRRRAG-PGAKLMAVVKANAYGHGAvevARALLEGGADGFAVATLDEALELREAGItaPILVLGG--- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259   108 IPCHQVADAVEQGtDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDddflypGQESGFALKVLPEIVAEIQNLPGLHL 187
Cdd:pfam01168  77 FPPEELALAAEYD-LTPTVDSLEQLEALAAAARRLGKPLRVHLKIDTG------MGRLGFRPEEALALLARLAALPGLRL 149
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16131259   188 AGL-THFPCLlwDEAvgKVLPTP-NLHTLIQARDQLAKSGIALEQLNApSATSCTslpLLAQYGVTHAEPGHALTGTIP 264
Cdd:pfam01168 150 EGLmTHFACA--DEP--DDPYTNaQLARFREAAAALEAAGLRPPVVHL-ANSAAI---LLHPLHFDMVRPGIALYGLSP 220
 
Name Accession Description Interval E-value
PLPDE_III_yhfX_like cd06811
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX; This subfamily is composed of the ...
1-382 0e+00

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX; This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.


Pssm-ID: 143486  Cd Length: 382  Bit Score: 655.88  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259   1 MFVEALKRQNPALISAALSLWQQGKIAPDSWVIDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYSG 80
Cdd:cd06811   1 MFLEALLKRNPALIEAALTLHQSGAIPPDTYVIDLDQIEENARLLAETAEKYGIELYFMTKQFGRNPFLARALLEAGIPG 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  81 IVAVDYKEARVMRRAGLPVAHQGHLVQIPCHQVADAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDDFLY 160
Cdd:cd06811  81 AVAVDFKEARALHEAGLPLGHVGHLVQIPRHQVPAVLAMRPEVITVYSLEKAREISDAAVELGRVQDVLLRVYGDEDTLY 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 161 PGQESGFALKVLPEIVAEIQNLPGLHLAGLTHFPCLLWDEAVGKVLPTPNLHTLIQARDQLAKSGIALEQLNAPSATSCT 240
Cdd:cd06811 161 PGQEGGFPLEELPAVLAAIKALPGIRIAGLTSFPCFLYDEEQGDIAPTPNLFTLLKAKELLEKRGIEILQLNAPSATSCA 240
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 241 SLPLLAQYGVTHAEPGHALTGTIPANQQGDQPERIAMLWLSEISHHFRGDSYCYGGGYYRRGHAQHALVFTPENQKITET 320
Cdd:cd06811 241 TLPLLAEYGVTHGEPGHALTGTTPLHAVGDQPEKPAMVYVSEVSHTFGGHSYCYGGGFYRRSHLKNALVGTDPDDASAHR 320
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16131259 321 NLkTVDDSSIDYTLPLAGE-FPVSSAVVLCFRTQIFVTRSDVVLVSGIHRGEPEIVGRYDSLG 382
Cdd:cd06811 321 AE-LLDPENIDYYGTLDGPeFAVGDTVIMAFRTQIFVTRSDVALVSGIASGKPRLVGIYDSQG 382
YhfX COG3457
Predicted amino acid racemase [Amino acid transport and metabolism];
26-370 2.94e-125

Predicted amino acid racemase [Amino acid transport and metabolism];


Pssm-ID: 442680 [Multi-domain]  Cd Length: 356  Bit Score: 365.28  E-value: 2.94e-125
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  26 IAPDSWVIDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYSGIVAVDYKEARVMRRAGLPvaHQGHL 105
Cdd:COG3457   1 IPPPTLVIDLDKIRENARRLVELAAKHGIELYGVTKQFGGNPEIAKALLDGGIKGIVDSRIKNLKKLKRAGIP--HPGHL 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 106 VQIPCHQVADAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDDflypgQESGFAlKVLPEIVAEIQNLPGL 185
Cdd:COG3457  79 LRIPMLSEVEEVVRYADISLNSELETARALSEAAKKQGKVHKVILMVDLGDL-----REGGFP-EELVDTVEEILKLPGI 152
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 186 HLAGL-THFPCLlwdeavGKVLPT-PNLHTLIQARDQL-AKSGIALEQLNAPSAtscTSLPLLAQ----YGVTHAEPGHA 258
Cdd:COG3457 153 ELAGLgTNLPCF------GGVLPTeENLGTLLELAELLeAKFGIKLPIVSGGNS---TSLPLLAEgtlpKGINHLRPGEA 223
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 259 LT-GTIPANQ-QGDQPERIAMLWLSEISHHFR--------------GDSYCYGggyyRRGHAQHALVFTPEnQKITETNL 322
Cdd:COG3457 224 LLlGTDPLNArPIPGLEQDAFVLVAEIIELKEkpsvpigeigrdafGNAPEFG----DRGIRKRAILAIGR-QDVDPEGL 298
                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 16131259 323 KTVDD------SSIDYtLPLAGEF-----PVSSAVVLCFRTQIFVTRSDVVLVSGIHRG 370
Cdd:COG3457 299 TPIDYgieilgASSDH-LILDVTDskedyKVGDTVVFCLRYQAFLTRSTSAYVEKIYSG 356
PLPDE_III cd06808
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme ...
38-257 5.41e-46

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity.


Pssm-ID: 143484 [Multi-domain]  Cd Length: 211  Bit Score: 156.71  E-value: 5.41e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  38 ILENGKRLIETARLyGIELYLMTKQFGrNPWLAEKLLALGySGIVAVDYKEARVMRRAGLPvaHQGHLVQIPC---HQVA 114
Cdd:cd06808   1 IRHNYRRLREAAPA-GITLFAVVKANA-NPEVARTLAALG-TGFDVASLGEALLLRAAGIP--PEPILFLGPCkqvSELE 75
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 115 DAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDdflYPGQeSGFALKVLPEIVAEIQNLPGLHLAGLTHFP 194
Cdd:cd06808  76 DAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRIDTGD---ENGK-FGVRPEELKALLERAKELPHLRLVGLHTHF 151
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16131259 195 CLLWDEAvgkVLPTPNLHTLIQARDQLAKSGIALEQLNAPSATSCTSLPLLAQYGVTHAEPGH 257
Cdd:cd06808 152 GSADEDY---SPFVEALSRFVAALDQLGELGIDLEQLSIGGSFAILYLQELPLGTFIIVEPGR 211
Ala_racemase_N pfam01168
Alanine racemase, N-terminal domain;
33-264 3.71e-27

Alanine racemase, N-terminal domain;


Pssm-ID: 460095 [Multi-domain]  Cd Length: 220  Bit Score: 107.31  E-value: 3.71e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259    33 IDVDQILENGKRLIETARlYGIELYLMTKQFGRNPWL---AEKLLALGYSGIVAVDYKEARVMRRAGL--PVAHQGHlvq 107
Cdd:pfam01168   1 IDLDALRHNLRRLRRRAG-PGAKLMAVVKANAYGHGAvevARALLEGGADGFAVATLDEALELREAGItaPILVLGG--- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259   108 IPCHQVADAVEQGtDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDddflypGQESGFALKVLPEIVAEIQNLPGLHL 187
Cdd:pfam01168  77 FPPEELALAAEYD-LTPTVDSLEQLEALAAAARRLGKPLRVHLKIDTG------MGRLGFRPEEALALLARLAALPGLRL 149
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16131259   188 AGL-THFPCLlwDEAvgKVLPTP-NLHTLIQARDQLAKSGIALEQLNApSATSCTslpLLAQYGVTHAEPGHALTGTIP 264
Cdd:pfam01168 150 EGLmTHFACA--DEP--DDPYTNaQLARFREAAAALEAAGLRPPVVHL-ANSAAI---LLHPLHFDMVRPGIALYGLSP 220
PLPDE_III_AR_like_1 cd06815
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily ...
33-245 1.58e-16

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.


Pssm-ID: 143490 [Multi-domain]  Cd Length: 353  Bit Score: 79.90  E-value: 1.58e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  33 IDVDQILENGKRLIETARLYGIELYLMTKQFGRNPWLAEKLLALGYSGIvavdyKEARV-----MRRAGLPVAHQghLVQ 107
Cdd:cd06815   6 INLSKIRHNAKVLVELCKSRGIEVTGVTKVVCGDPEIAEALLEGGITHL-----ADSRIenlkkLKDLGISGPKM--LLR 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 108 IPC-HQVADAVEQgTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDDdflypGQEsgfalKVLPE----IVAEIQNL 182
Cdd:cd06815  79 IPMlSEVEDVVKY-ADISLNSELETIKALSEEAKKQGKIHKIILMVDLGD-----LRE-----GVLPEdlldFVEEILKL 147
                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16131259 183 PGLHLAGL-THFPCLlwdeavGKVLPTP-NLHTLIQARDQL-AKSGIALEQLnapSATSCTSLPLL 245
Cdd:cd06815 148 PGIELVGIgTNLGCY------GGVLPTEeNMGKLVELKEEIeKEFGIKLPII---SGGNSASLPLL 204
Dsd1 COG3616
D-serine deaminase, pyridoxal phosphate-dependent [Amino acid transport and metabolism];
32-298 5.57e-10

D-serine deaminase, pyridoxal phosphate-dependent [Amino acid transport and metabolism];


Pssm-ID: 442834 [Multi-domain]  Cd Length: 357  Bit Score: 60.15  E-value: 5.57e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  32 VIDVDQILENGKRLIETARLYGIELYLMTKQFgRNPWLAEKLLALGYSGIVAVDYKEARVMRRAGLP---VAHQghLVQI 108
Cdd:COG3616  12 VLDLDALERNIARMAARAAAHGVRLRPHGKTH-KSPELARRQLAAGAWGITVATLAEAEVLAAAGVDdilLAYP--LVGP 88
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 109 P-CHQVADAVEQGTDV-ITVFTLDKAREVSAAAVKAGRIQSVLLKVysddDFlyPGQESGfalkVLP-----EIVAEIQN 181
Cdd:COG3616  89 AkLARLAALARAGARLtVLVDSVEQAEALAAAAAAAGRPLRVLVEL----DV--GGGRTG----VRPpeaalALARAIAA 158
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 182 LPGLHLAGL-THfpcllwdEAVGKVLPTPN---------LHTLIQARDQLAKSGIALEQLNA---PSATSCTSLPllaqy 248
Cdd:COG3616 159 SPGLRLAGLmTY-------EGHIYGADDAEerraaareeLARLAAAAEALRAAGLPCPIVSGggtPTFDFVADLP----- 226
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
gi 16131259 249 GVTHAEPGHALTGtiPANQQG---DQPERIAM-LWLSEISHHFRGDSYCYGGGY 298
Cdd:COG3616 227 GVTELRPGSYVFH--DAGYYRygvCFPFDPALsVLATVVSRPEPGRAILDAGSK 278
PLPDE_III_AR cd00430
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; This family includes ...
69-195 1.46e-07

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. AR and other members of this family require dimer formation and the presence of the PLP cofactor for catalytic activity. Fungal ARs and eukaryotic serine racemases, which are fold types I and II PLP-dependent enzymes respectively, are excluded from this family.


Pssm-ID: 143481 [Multi-domain]  Cd Length: 367  Bit Score: 52.88  E-value: 1.46e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  69 LAEKLLALGYSGI-VA-VDykEARVMRRAG--LPVahqghLV--QIPCHQVADAVEQGTDViTVFTLDKAREVSAAAVKA 142
Cdd:cd00430  44 VAKALEEAGADYFaVAtLE--EALELREAGitAPI-----LVlgGTPPEEAEEAIEYDLTP-TVSSLEQAEALSAAAARL 115
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 16131259 143 GRIQSVLLKVysdddflypgqES-----GFALKVLPEIVAEIQNLPGLHLAGL-THFPC 195
Cdd:cd00430 116 GKTLKVHLKI-----------DTgmgrlGFRPEEAEELLEALKALPGLELEGVfTHFAT 163
PLPDE_III_LS_D-TA_like cd06820
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine ...
32-256 6.27e-04

Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like; This subfamily is composed of uncharacterized bacterial proteins with similarity to low specificity D-threonine aldolase (D-TA), which is a fold type III PLP-dependent enzyme that catalyzes the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Low specificity D-TAs show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exhibit full catalytic activity.


Pssm-ID: 143494 [Multi-domain]  Cd Length: 353  Bit Score: 41.53  E-value: 6.27e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259  32 VIDVDQILENGKRLIETARLYGIELYLMTKQFgRNPWLAEKLLALGYSGIVAVDYKEARVMRRAGL-------PVAHQGH 104
Cdd:cd06820   7 LIDLDRLERNIARMQAYADAHGLSLRPHIKTH-KSPEIARLQLAAGAIGITVATVGEAEVMADAGLsdifiayPIVGRQK 85
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 105 LVQIpchqvADAVEQGTDVITVFTLDKAREVSAAAVKAGRIQSVLLKVYSDddflypGQESGfalkVLPE-----IVAEI 179
Cdd:cd06820  86 LERL-----RALAERVTLSVGVDSAEVARGLAEVAEGAGRPLEVLVEVDSG------MNRCG----VQTPedavaLARAI 150
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16131259 180 QNLPGLHLAGLTHFPCLLWDEAVGKVLPTPNLHTLIQARDQLAKSGIaleqlnAPSATSCTSLPLLAQY----GVTHAEP 255
Cdd:cd06820 151 ASAPGLRFRGIFTYPGHSYAPGALEEAAADEAEALLAAAGILEEAGL------EPPVVSGGSTPTLWRShevpGITEIRP 224

                .
gi 16131259 256 G 256
Cdd:cd06820 225 G 225
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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